refactor RAG, adding rag module

[GdoongMathew]

Summary

• move rag related data_pipeline, ollama model validation function, and RAG to dedicated rag module.
• removing ollama_patch.
• move get_file_content and related functions to repository module.
• Remove duplicated for loop in RAG._validate_and_filter_embeddings.

[gemini-code-assist]

Caution

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